> Cornelius Hunter wrote:
> COuld I ask you to support your claims, at least the once which make
> claims about science? Such as the Herv data? How again does it disprove
> common descent? Are you sure you are not using what is known as a 'naive
> falsification' approach here?
>
> Present your argument. I will see what science has found out about it.

Actually, HERVs do not disprove CD. That is not possible because it is
behind a mote. HERVs merely disprove predictions of CD.

This is a fine example. Evolution predicts that an homologous HERV in
chimpanzees, bonobos and gorillas will also be found in humans. The
prediction is false. Wild after-the-fact speculation by dedicated
evolutionists who presuppose their theory is true doesn't count. Anybody can
make up just-so stories to rescue theories like geocentrism. So please,
spare us the idle speculation that cannot be falsified.

Preston:

> Cornelius and all,
>
> I have cut out some stuff that I'm not responding to.
>
> P.
>
>>
>>>>>Let me ask you about about related evidence. Are you not at all
>>>>>struck by the obvious assembly of human chr 2 (if I remember right)
>>>>>from 2 ape chromosomes?
>>>>>Why are there 2 sets of telomere repeats
>>>>>fused head to head internally at the expected position?
>>>>
>>>>Probably because there was a fusion event in the human lineage.
>>>
>>>If so, then the human lineage started out looking very much like the
>>>ape lineage. Why would that be so on your alternate hypothesis,
>>>whatever its is?
>>
>>Folks this is a great example. We have evidence that the human lineage
>>underwent a chromosomal fusion. OK, fine. But this, therefore, is
>>compelling evidence for evolution? How can this be? This has nothing to do
>>with common descent or evolution.
>
> When you say it is only evidence for a fusion in the human line, you
> ignore the fact that the 2 partners for the fusion look extremely like 2
> chromosomes in the closest related species. You simply discard that part
> of the evidence.

Not at all, but that's nothing new. There are all kinds of similarities
between the human and chimp. What is it, 97% DNA sequence identity?

Another way to frame this is as a
> violation of parsimony. You multiply entities, in this case chromosomes,
> unnecessarily, positing 2 primordial human chromosomes when the extremely
> similar ape chromosomes are there before you.

Your argument collapses to this: There are a pair of chromosomes in the
human and chimp with similar G-banding. This must be compelling evidence for
evolution.

> Logically, those 2 human-like chromosomes could have been present in any
> one of a zillion distant species or present nowhere.

More Bernoullian logic and its false dichotomy. Anything is possible, so
random chance is the null hypothesis. And if the null hypothesis is false,
then naturalism is the only other choice.

>But there they are in the one species where they would be predicted to be
>by common descent, and you say this has no significance as evidence. I'm
>sorry, but this just seems tendentious to me. I'm trying to understand your
>refusal to connect the two parts of the evidence, but I can't.

It is evidence for CD in the same way that are other similar features of the
chimp and human. So you want there to be no similarities between species
(random design). By the way, if that were true, evolutionists would be
arguing that only natural selection would create such unique designs, for it
considers only survival whereas surely God would use a pattern.

>>And when this is pointed out, the claim is defended by asking for a better
>>explanation. If you can't supply the rationalist with an explanation, then
>>his is right.
>
> I didn't say that. I just asked if you had another hypothesis. Cornelius,
> surely it is the common practice in science to try to provide a better
> hypothesis. I wouldn't ask for one if you were a layman, but since you are
> a scientist it seems like a reasonable request. Since you reject a bit of
> evidence that looks obviously relevant to me and I would guess others, I
> wondered if you are making the judgement in comparison to another
> hypothesis which you think is much better. If you have one, I'd like to
> know what is it and why is it better? If you don't have one, why shouldn't
> I stick with one that looks pretty good? I haven't asserted certainty at
> any point.

>>>For the record, for a long time I was rather
>>>non-committal on the issue despite being raised in a fundamentalist
>>>background, but the genomic evidence seems pretty convincing to me in
>>>that common descent seems to account for a lot of things very nicely.
>>
>>Fair enough, but so does geocentrism. The problem lies in the details. I
>>can't respond to statements like "seems convincing." The key question is:
>>why do you think this? You seem to be unfamiliar with details such as
>>HERVs and mutational hotspots.
>
> I'm familiar enough with both concepts. I haven't covered the whole
> literature. This is not the main thing I do. I've looked at a number of
> papers where large groups of insertions were examined across multiple
> species. In every case the proportion of insertions with an anomalous
> phylogenetic pattern was very small. Most of them are accountable as
> lineage sorting of an element that is not fully fixed. Since their
> fixation is slow and uncertain due to their neutrality, this seems like a
> quite reasonable account when the speciation times are close. A few were
> found to be likely homoplasies (independent insertions), but not the
> large proportion you insist on.

I didn't mean to insist on large proportions. I don't have the statistics at
hand. My point is there are HERVs that falsify predictions of CD, and heroic
speculation is required to patch things up. I'm not even saying that the
speculation is necessarily false. But we certainly cannot point to HERVs as
compelling evidence if, when they fail to deliver we then feel free to
contrive speculation to save the day. If you are going to patch things up
this way, then please don't turn around and tell me they provide this great
fulfilled prediction. It can't be a prediction if it is explained away when
it fails. That's not a prediction.

As to
> hotspots, if you are talking about hotspots for point mutations, they are
> irrelevant to transposable elements.

Agreed.

>I've seen reference to a couple of insertion hotspots for TEs, not
>thousands. If there are HERVs that are grossly anomalous in their pattern,
>I've never seen them referred to. There's no way I can evaluate it if you
>won't provide references.

Pim's reference above is a fine example.

I don't have time to search a large literature on
> a concept that isn't easily defined for a search. When you make these kind
> of assertions, it really is customary to provide references. If you want
> the ones I refer to, I have them. If this is from your own research, why
> don't you publish a paper?
>
>
>>
>>>>Actually, that burden is on you, not me. You are the one who is
>>>>making the claim that a duplicated mutation is conspicuous, and of
>>>>low probability in a vast pool of repeated mutations that cannot be
>>>>due to common descent (that is a non intuitive claim). I believe you
>>>>will fail to make the point because there literally are many more of
>>>>these mutations that cannot be due to common descent. Have you
>>>>looked at them?
>>>
>>>I'm not aware of any that can't be explained. Examples please.
>>
>>independent mutations are common across the board--viruses, bacteria,
>>higher organisms. Within the field this is not controversial (it is a
>>biological fact).
>>
>
> It is not my impression that this is true for transposable elements. Every
> discussion I have seen in the literature has concluded that independent
> insertions of the same element at the same position are rare.

Agreed, although this used to be what was believed about point mutations as
well.

>>>>Everything that is known about LINE elements, endogenous
>>>>>retroviruses, Alu elements indicates that they only have mild
>>>>>biases about target locations. To suggest that this is analogous to
>>>>>mutational hotspots is ludicrous. There is one example of an HERV
>>>>>which is present in only one copy in human and several ape genomes.
>>>>>In all it is at the same position.
>>>>
>>>>Yes, and there are also HERVs at the same positions that do not
>>>>follow the common descent pattern. Again, this is special pleading.
>>>
>>>Again, examples, please.
>>
>>Same answer as above. There are HERVs found in the human and distant
>>species like old world monkeys, yet not in chimps or gorillas. Then there
>>are HERVs found in widespread species but not humans. Both falsify the
>>prediction of common descent.
>
> I thought you liked tentative probabilistic conclusions. That sounds like
> an assertion of absolute certainty.

Yes, I am certain that a prediction of CD has been falsified. If you want to
say it never really was a prediction in the first place, then that's fine
with me.

>Deletions do happen.

HERVs do not "delete" and leave a clean, pre-insertion site. That is one of
the reasons why they were heralded as such great evidence for CD--until,
that is, "anomalous" ones were discovered which violate CD.

>>>Do you have any alternative hypothesis for these things that doesn't
>>>reduce to "God just did it that way?" I don't mean to be offensive,
>>>but if special creation of every species is your hypothesis, I don't
>>>see how you avoid that, and as Ted pointed out, that is the most
>>>unfalsifiable hypothesis of all.
>>
>>No offense taken. However, I do disagree with the unfalsifiable part. All
>>that is needed is compelling evidence for evolution.
>
> I don't see why. No matter how good the evidence for evolution might be,
> one could always still say "God just did it that way."

No offense intended, but this is a typical evolutionist strawman.

>You might change your mind, but it wouldn't be because special creation had
>been falsified.
>
> What would you regard as compelling evidence for evolution?

examples:
1. Formation of a cell in the lab.
2. Scientific description of how the DNA code evolved.
3. Scientific description of how Histone IV evolved.
4. Scientific description of how echolocation in bats evolved.
5. Scientific description of how the human brain evolved.
6. Scientific explanation of how macro evolution works in spite of the fact
that small scale adaptation seems to be limited.
7. Scientific explanation of how the evolutionary process evolves so as to
make evolution possible.
8. Scientific explanation of how massive convergence happens in evolution.
How does evoltuion find same solutions in the astronomical design space?
9. Scientific explanation for non homologous development pathways and genes
for homologous structures in cousin species.

> Finally, do you see theological problems with common descent per se?

No.

> Omit the Darwinian mechanism and the bugaboo of randomness, bring in ID
> type insertions of new sequences. You still have to have animal death
> before the Fall. Do you see theological problems with that?

No, not necessarily.

> Shalom,
>
> Preston

> Cornelius,
>
> I'm working on a response that I owe you.
>
> This response of yours (and the recent one about the chromosome fusions)
> is helpful in laying out some of our fundamental differences. This is
> sort of what I was trying to get at in point out different "thresholds of
> what's compelling". I'm not sure that I would put it exactly the way you
> put it, but it makes the point. I don't really mind being put in the
> rationalist camp as you describe it. I do believe that God made a
> knowable, lawfully ordered world where we can discern that lawful order.
> I'm an empiricist but an empiricist driven to see patterns, regularities,
> laws, etc. Having a theoretical framework (like common ancestry) is an
> important value in my science.

Right.

>As long as it's a productive framework (even with anomalies), it's useful
>(and as such it "probably" true).

Geocentrism, flat earth, and many other false theories are useful.

>I think philosophers of science refer to these sorts of things as
>epistemic values. And yes, different epistemic values produce differences
>in "science".

Which is all well and good. But when you bring truth claims into the picture
then that is a horse of a different color.

I think the majority view among practicing scientists
> leans toward my "rationalism" compared to your "moderate empiricists".
>
> So when you admit that common ancestry is consistent with the various
> data we present (nested hierarchies, cytochrome c sequence comparisons,
> ape-like chromosome fusions, pseudogenes), I think that's all I ask.
> You're "less certain" because you don't seem to value having the guiding
> overarching theoretical framework as much as some of us do.

What is important to add to this picture, however, are the many, many
problems with evolution. Overlooking those is the price one pays for having
that overarching theoretical framework.